I would ask anyone with ideas on how to increase challenge to add to this discussion. :D

So having played a ton of brutal matches to 99 now and experimented with a bunch of builds, I think one thing that needs to be done to increase challenge is tweaks to enemy abilities at higher difficulties. I think that:
1. They should construct faster in higher difficulties, allowing them more opportunity to recover from attacks
2. Since soon the flooding build will be viable it might be worth giving the enemy the ability to build some "floating buildings" that are also immune to ignite damage, specialty buildings that can give them a chance to counter flood and ignite builds.
3. Now that projectile accuracy is better I think that a Kamikaze tank would be a good add for the enemy forces, It spawns, makes a marker on the map, and heads for that marker at high speed ignoring all minions. If it reaches it it explodes causing major corruption increase.
4. Give builders a longer range so its not so easy to just destroy them along with their constructs. This will add with increased build speed to make them more dangerous and harder to control.
5. Add a stronger defensive building thats able to effectively deal with minions. I'd say a weapon that uses the Commanders burst power with maybe 10-15 second cooldown.
6. Find a way to make it not so easy to keep corruption at 0. Either increase corruption cleanse resistance, or increase corruption gain as the match goes on. It would make a lot of sense to me if it became harder to win the longer the match took, that's just common difficulty scaling, and will prevent the ability to just muddle through with a half assed build.
7. Ive said this before in discord but I still strongly feel like Diamond Core and Webbed Menace should be switched. Diamond Core makes a lot of sense to me as an inherent scaling power that has universally useful effects, whereas webbed menace feels to me more like a crutch that gives you an excuse not to get better at the game. They also make the "dont cast any spells for 45 seconds" challenge a joke lol
8. Continuing my thought about the kamikaze tank, I think that in high difficulties multiple buildings and units should be given a "self destruct" feature. Once they take enough damage they begin a countdown andif theyre not destroyed before the countdown is reached they explode causing corruption gain.
9. Challenge Mode: You are given a flat amount of Shards, 5 rerolls, and 3 choices for spells. You pick 4 spells at the start of the run with your rerolls, then use your shards as you see fit. You have to play 5 regions at a time regardless of modifiers, and you have to finish level 99 without any extra shards rewards, and stat bonuses are rare, like once every 5 regions. You get a blessing every 20 regions, with a blessing upgrade choice every 15 after. (Just numbers pulled from feeling, they can be tweaked however)

The biggest issue I see with any type of difficulty scaling is Resources. Resources wont drop unless youre effectively destroying the enemy quickly, but if you are they wont have any chance to recover unless they win through reinforcements. If you raise resources it doesnt matter cause theyll just drain when the enemy has too few constructs, so it makes no difference.
That said, if it becomes much harder to drain the enemies resourcesthrough base destruction that would give more reason to add extra methods to reduce it. As it stands theres no reason to bother with "reduce enemy resources" stats, but those could become much more useful in high difficulty